Starting phenix.real_space_refine on Fri Aug 22 21:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.map" model { file = "/net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hs3_34984/08_2025/8hs3_34984.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5223 2.51 5 N 1453 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8258 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1709 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1761 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 4, 'n_c_alpha_c_only': 44, 'truncation_to_alanine': 46} Link IDs: {'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 50 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 561 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 3, 'ARG:plan': 11, 'ASP:plan': 1, 'GLU:plan': 2, 'TRP:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 180 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8258 At special positions: 0 Unit cell: (95.68, 115.648, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1523 8.00 N 1453 7.00 C 5223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 436.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.922A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.771A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.531A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.585A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.819A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.999A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.543A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 42 Processing helix chain 'R' and resid 56 through 80 WARNING: missing atoms! removed outlier: 3.579A pdb=" N LEU R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 113 Proline residue: R 107 - end of helix removed outlier: 4.222A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 133 removed outlier: 3.892A pdb=" N LEU R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 153 removed outlier: 3.614A pdb=" N VAL R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 185 removed outlier: 3.530A pdb=" N SER R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 206 Processing helix chain 'R' and resid 206 through 224 Processing helix chain 'R' and resid 229 through 231 No H-bonds generated for 'chain 'R' and resid 229 through 231' Processing helix chain 'R' and resid 232 through 254 removed outlier: 3.572A pdb=" N ARG R 236 " --> pdb=" O GLY R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.100A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 288 removed outlier: 3.726A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 308 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.709A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.857A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.963A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.987A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.695A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.558A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.727A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.920A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.684A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.729A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.670A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.352A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.815A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.742A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2716 1.34 - 1.46: 1986 1.46 - 1.58: 3626 1.58 - 1.70: 4 1.70 - 1.81: 83 Bond restraints: 8415 Sorted by residual: bond pdb=" CB PRO R 226 " pdb=" CG PRO R 226 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" CB PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.38e+00 bond pdb=" CB PRO R 271 " pdb=" CG PRO R 271 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.57e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.636 -0.144 5.00e-02 4.00e+02 8.31e+00 bond pdb=" CG PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.62e+00 ... (remaining 8410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 11288 3.31 - 6.61: 67 6.61 - 9.92: 7 9.92 - 13.22: 4 13.22 - 16.53: 3 Bond angle restraints: 11369 Sorted by residual: angle pdb=" CA PRO R 268 " pdb=" N PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 112.00 95.47 16.53 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" CD PRO R 271 " ideal model delta sigma weight residual 112.00 97.72 14.28 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 97.74 14.26 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO R 226 " pdb=" N PRO R 226 " pdb=" CD PRO R 226 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N PRO R 268 " pdb=" CD PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 103.20 95.71 7.49 1.50e+00 4.44e-01 2.49e+01 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4174 16.75 - 33.49: 557 33.49 - 50.24: 183 50.24 - 66.99: 24 66.99 - 83.74: 10 Dihedral angle restraints: 4948 sinusoidal: 1793 harmonic: 3155 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CA SER B 334 " pdb=" C SER B 334 " pdb=" N PHE B 335 " pdb=" CA PHE B 335 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1054 0.056 - 0.112: 220 0.112 - 0.168: 17 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" C PRO R 271 " pdb=" CB PRO R 271 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR R 255 " pdb=" N THR R 255 " pdb=" C THR R 255 " pdb=" CB THR R 255 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP R 267 " -0.126 5.00e-02 4.00e+02 1.75e-01 4.87e+01 pdb=" N PRO R 268 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO R 268 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO R 268 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.099 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO S 75 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 270 " -0.074 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO R 271 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO R 271 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 271 " -0.056 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 212 2.69 - 3.24: 7695 3.24 - 3.80: 13427 3.80 - 4.35: 16816 4.35 - 4.90: 29017 Nonbonded interactions: 67167 Sorted by model distance: nonbonded pdb=" ND1 HIS R 126 " pdb=" NE2 HIS R 126 " model vdw 2.141 2.560 nonbonded pdb=" O MET A 18 " pdb=" ND2 ASN A 22 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASN R 133 " pdb=" OG SER R 286 " model vdw 2.277 3.040 ... (remaining 67162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 8417 Z= 0.161 Angle : 0.751 16.527 11373 Z= 0.407 Chirality : 0.045 0.280 1296 Planarity : 0.009 0.175 1437 Dihedral : 16.983 83.736 2936 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.36 % Allowed : 29.33 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.25), residues: 1106 helix: 0.18 (0.27), residues: 349 sheet: -1.39 (0.31), residues: 272 loop : -1.34 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 260 TYR 0.015 0.001 TYR S 178 PHE 0.035 0.002 PHE S 80 TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 8415) covalent geometry : angle 0.75107 (11369) SS BOND : bond 0.00487 ( 2) SS BOND : angle 0.27578 ( 4) hydrogen bonds : bond 0.18863 ( 387) hydrogen bonds : angle 7.19641 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.315 Fit side-chains REVERT: A 197 LYS cc_start: 0.7589 (mttm) cc_final: 0.7110 (mttm) REVERT: A 198 MET cc_start: 0.8127 (mtp) cc_final: 0.7910 (mtp) REVERT: B 292 PHE cc_start: 0.8725 (m-80) cc_final: 0.8401 (m-80) REVERT: S 60 TYR cc_start: 0.8936 (m-80) cc_final: 0.8456 (m-80) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.0884 time to fit residues: 14.3678 Evaluate side-chains 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121889 restraints weight = 9628.006| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.82 r_work: 0.3309 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8417 Z= 0.135 Angle : 0.545 10.947 11373 Z= 0.287 Chirality : 0.042 0.167 1296 Planarity : 0.005 0.087 1437 Dihedral : 4.871 66.368 1209 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.49 % Allowed : 29.10 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.25), residues: 1106 helix: 0.86 (0.28), residues: 355 sheet: -1.22 (0.30), residues: 281 loop : -1.02 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 190 TYR 0.023 0.001 TYR S 178 PHE 0.013 0.001 PHE R 250 TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8415) covalent geometry : angle 0.54502 (11369) SS BOND : bond 0.00549 ( 2) SS BOND : angle 0.91832 ( 4) hydrogen bonds : bond 0.04065 ( 387) hydrogen bonds : angle 5.18550 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.194 Fit side-chains REVERT: A 22 ASN cc_start: 0.6860 (m-40) cc_final: 0.6591 (m110) REVERT: A 197 LYS cc_start: 0.7838 (mttm) cc_final: 0.7637 (mttm) REVERT: A 247 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: B 262 MET cc_start: 0.8178 (mmt) cc_final: 0.7914 (mmt) REVERT: B 292 PHE cc_start: 0.8756 (m-80) cc_final: 0.8227 (m-80) outliers start: 21 outliers final: 14 residues processed: 128 average time/residue: 0.0734 time to fit residues: 13.6160 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114782 restraints weight = 9770.462| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.83 r_work: 0.3230 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 8417 Z= 0.295 Angle : 0.665 10.857 11373 Z= 0.351 Chirality : 0.048 0.237 1296 Planarity : 0.005 0.062 1437 Dihedral : 4.931 41.498 1203 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 6.29 % Allowed : 25.89 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.25), residues: 1106 helix: 0.84 (0.28), residues: 353 sheet: -1.52 (0.30), residues: 274 loop : -1.05 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.024 0.002 TYR S 178 PHE 0.026 0.002 PHE R 250 TRP 0.021 0.002 TRP S 47 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 8415) covalent geometry : angle 0.66532 (11369) SS BOND : bond 0.00653 ( 2) SS BOND : angle 1.03929 ( 4) hydrogen bonds : bond 0.04236 ( 387) hydrogen bonds : angle 5.13795 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7144 (m-40) cc_final: 0.6801 (m110) REVERT: A 192 LYS cc_start: 0.9226 (ttpp) cc_final: 0.8983 (ttpp) REVERT: A 247 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7589 (mtp) REVERT: B 45 MET cc_start: 0.8888 (mmt) cc_final: 0.8044 (mmt) REVERT: B 314 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7324 (ptt180) REVERT: S 22 CYS cc_start: 0.6413 (t) cc_final: 0.6028 (t) REVERT: S 60 TYR cc_start: 0.8966 (m-80) cc_final: 0.8659 (m-80) REVERT: S 113 GLN cc_start: 0.7886 (tp40) cc_final: 0.7429 (tp-100) REVERT: S 180 MET cc_start: 0.8092 (ttp) cc_final: 0.7813 (ttp) REVERT: S 218 MET cc_start: 0.8141 (ttm) cc_final: 0.7719 (ttm) outliers start: 53 outliers final: 36 residues processed: 147 average time/residue: 0.0863 time to fit residues: 17.7334 Evaluate side-chains 144 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120115 restraints weight = 9806.822| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.88 r_work: 0.3296 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8417 Z= 0.130 Angle : 0.521 7.224 11373 Z= 0.275 Chirality : 0.043 0.179 1296 Planarity : 0.004 0.053 1437 Dihedral : 4.390 35.025 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.46 % Allowed : 27.08 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.26), residues: 1106 helix: 1.20 (0.28), residues: 353 sheet: -1.46 (0.28), residues: 294 loop : -0.93 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.022 0.001 TYR S 178 PHE 0.010 0.001 PHE R 250 TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS R 273 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8415) covalent geometry : angle 0.52126 (11369) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.72801 ( 4) hydrogen bonds : bond 0.03134 ( 387) hydrogen bonds : angle 4.75735 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7152 (m-40) cc_final: 0.6823 (m110) REVERT: A 247 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7477 (mtp) REVERT: B 45 MET cc_start: 0.8710 (mmt) cc_final: 0.8167 (mmt) REVERT: B 273 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 292 PHE cc_start: 0.8932 (m-80) cc_final: 0.8355 (m-80) REVERT: B 314 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7291 (ptt180) REVERT: S 22 CYS cc_start: 0.6370 (t) cc_final: 0.6011 (t) REVERT: S 218 MET cc_start: 0.8060 (ttm) cc_final: 0.7515 (ttm) outliers start: 46 outliers final: 29 residues processed: 148 average time/residue: 0.0695 time to fit residues: 14.5568 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.165399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121138 restraints weight = 9557.973| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.84 r_work: 0.3302 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8417 Z= 0.111 Angle : 0.500 6.369 11373 Z= 0.262 Chirality : 0.042 0.180 1296 Planarity : 0.004 0.059 1437 Dihedral : 4.146 29.823 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.46 % Allowed : 28.15 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 1106 helix: 1.34 (0.29), residues: 354 sheet: -1.33 (0.29), residues: 294 loop : -0.84 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.020 0.001 TYR S 178 PHE 0.015 0.001 PHE R 131 TRP 0.010 0.001 TRP R 175 HIS 0.003 0.001 HIS R 273 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8415) covalent geometry : angle 0.49992 (11369) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.64830 ( 4) hydrogen bonds : bond 0.02884 ( 387) hydrogen bonds : angle 4.56168 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6966 (m-40) cc_final: 0.6578 (m110) REVERT: A 247 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7410 (mtp) REVERT: B 292 PHE cc_start: 0.8931 (m-80) cc_final: 0.8345 (m-80) REVERT: B 314 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7261 (ptt180) REVERT: R 270 MET cc_start: 0.7023 (ptt) cc_final: 0.6797 (ptt) REVERT: S 22 CYS cc_start: 0.6284 (t) cc_final: 0.5885 (t) REVERT: S 210 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6449 (pp20) REVERT: S 218 MET cc_start: 0.8107 (ttm) cc_final: 0.7688 (ttm) outliers start: 46 outliers final: 35 residues processed: 153 average time/residue: 0.0814 time to fit residues: 17.7819 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 HIS Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123380 restraints weight = 9455.537| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.72 r_work: 0.3331 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8417 Z= 0.103 Angle : 0.500 10.334 11373 Z= 0.259 Chirality : 0.042 0.182 1296 Planarity : 0.004 0.058 1437 Dihedral : 4.036 28.429 1203 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.46 % Allowed : 28.27 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.26), residues: 1106 helix: 1.44 (0.29), residues: 354 sheet: -1.22 (0.29), residues: 292 loop : -0.83 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE R 254 TRP 0.010 0.001 TRP R 175 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8415) covalent geometry : angle 0.50006 (11369) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.56790 ( 4) hydrogen bonds : bond 0.02763 ( 387) hydrogen bonds : angle 4.43484 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.214 Fit side-chains REVERT: A 247 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7395 (mtp) REVERT: B 130 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 152 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 292 PHE cc_start: 0.8907 (m-80) cc_final: 0.8379 (m-80) REVERT: B 314 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7253 (ptt180) REVERT: R 139 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6285 (mp) REVERT: S 22 CYS cc_start: 0.6174 (t) cc_final: 0.5791 (t) REVERT: S 210 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6515 (pp20) REVERT: S 218 MET cc_start: 0.8115 (ttm) cc_final: 0.7636 (ttm) outliers start: 46 outliers final: 33 residues processed: 153 average time/residue: 0.0813 time to fit residues: 17.8489 Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 HIS Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115305 restraints weight = 9687.577| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.28 r_work: 0.3150 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8417 Z= 0.255 Angle : 0.624 9.960 11373 Z= 0.328 Chirality : 0.047 0.202 1296 Planarity : 0.005 0.061 1437 Dihedral : 4.546 30.457 1203 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.41 % Allowed : 28.15 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.26), residues: 1106 helix: 1.13 (0.28), residues: 354 sheet: -1.43 (0.29), residues: 279 loop : -0.91 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.022 0.002 TYR S 178 PHE 0.024 0.002 PHE R 250 TRP 0.016 0.002 TRP S 47 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 8415) covalent geometry : angle 0.62393 (11369) SS BOND : bond 0.00542 ( 2) SS BOND : angle 0.87567 ( 4) hydrogen bonds : bond 0.03640 ( 387) hydrogen bonds : angle 4.76201 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6835 (m-40) cc_final: 0.6478 (m110) REVERT: A 247 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7410 (mtp) REVERT: B 152 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 292 PHE cc_start: 0.9018 (m-80) cc_final: 0.8404 (m-80) REVERT: B 314 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7197 (ptt180) REVERT: R 136 CYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5737 (p) REVERT: S 22 CYS cc_start: 0.6468 (t) cc_final: 0.6055 (t) REVERT: S 218 MET cc_start: 0.8262 (ttm) cc_final: 0.7735 (ttm) outliers start: 54 outliers final: 38 residues processed: 150 average time/residue: 0.0825 time to fit residues: 17.8950 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123785 restraints weight = 9420.215| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.88 r_work: 0.3239 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8417 Z= 0.119 Angle : 0.526 10.011 11373 Z= 0.274 Chirality : 0.042 0.167 1296 Planarity : 0.004 0.054 1437 Dihedral : 4.186 26.896 1203 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.51 % Allowed : 29.93 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 1106 helix: 1.31 (0.29), residues: 354 sheet: -1.36 (0.29), residues: 294 loop : -0.79 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE R 250 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS R 273 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8415) covalent geometry : angle 0.52482 (11369) SS BOND : bond 0.00413 ( 2) SS BOND : angle 1.88045 ( 4) hydrogen bonds : bond 0.02906 ( 387) hydrogen bonds : angle 4.55374 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6790 (m-40) cc_final: 0.6390 (m110) REVERT: A 247 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7333 (mtp) REVERT: B 130 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 152 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7761 (mp) REVERT: B 292 PHE cc_start: 0.8949 (m-80) cc_final: 0.8323 (m-80) REVERT: B 314 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7116 (ptt180) REVERT: S 22 CYS cc_start: 0.6320 (t) cc_final: 0.5917 (t) REVERT: S 218 MET cc_start: 0.8034 (ttm) cc_final: 0.7613 (ttm) outliers start: 38 outliers final: 32 residues processed: 140 average time/residue: 0.0759 time to fit residues: 15.3406 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121903 restraints weight = 9474.182| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.00 r_work: 0.3239 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8417 Z= 0.130 Angle : 0.532 11.021 11373 Z= 0.275 Chirality : 0.042 0.159 1296 Planarity : 0.004 0.060 1437 Dihedral : 4.122 27.834 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.75 % Allowed : 29.81 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.26), residues: 1106 helix: 1.30 (0.28), residues: 357 sheet: -1.33 (0.29), residues: 284 loop : -0.75 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.020 0.001 TYR S 178 PHE 0.020 0.001 PHE R 131 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8415) covalent geometry : angle 0.53159 (11369) SS BOND : bond 0.00476 ( 2) SS BOND : angle 1.57479 ( 4) hydrogen bonds : bond 0.02919 ( 387) hydrogen bonds : angle 4.47716 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6792 (m-40) cc_final: 0.6386 (m110) REVERT: A 247 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7342 (mtp) REVERT: B 130 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 152 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7795 (mp) REVERT: B 314 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7108 (ptt180) REVERT: S 22 CYS cc_start: 0.6304 (t) cc_final: 0.5895 (t) REVERT: S 218 MET cc_start: 0.8090 (ttm) cc_final: 0.7669 (ttm) outliers start: 40 outliers final: 31 residues processed: 142 average time/residue: 0.0791 time to fit residues: 16.3680 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124735 restraints weight = 9425.344| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.96 r_work: 0.3275 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8417 Z= 0.109 Angle : 0.512 10.863 11373 Z= 0.265 Chirality : 0.042 0.160 1296 Planarity : 0.004 0.058 1437 Dihedral : 3.992 27.127 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.16 % Allowed : 30.40 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.26), residues: 1106 helix: 1.43 (0.29), residues: 354 sheet: -1.25 (0.29), residues: 294 loop : -0.74 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.019 0.001 TYR S 178 PHE 0.010 0.001 PHE R 250 TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8415) covalent geometry : angle 0.51139 (11369) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.39105 ( 4) hydrogen bonds : bond 0.02723 ( 387) hydrogen bonds : angle 4.38259 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6761 (m-40) cc_final: 0.6378 (m110) REVERT: A 247 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7318 (mtp) REVERT: B 76 ASP cc_start: 0.8003 (p0) cc_final: 0.7468 (p0) REVERT: B 130 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 152 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7829 (mp) REVERT: B 292 PHE cc_start: 0.8920 (m-80) cc_final: 0.8304 (m-80) REVERT: B 314 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7128 (ptt180) REVERT: S 22 CYS cc_start: 0.6270 (t) cc_final: 0.5866 (t) REVERT: S 218 MET cc_start: 0.8029 (ttm) cc_final: 0.7614 (ttm) outliers start: 35 outliers final: 28 residues processed: 138 average time/residue: 0.0807 time to fit residues: 16.2093 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.0030 chunk 30 optimal weight: 0.0970 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129337 restraints weight = 9360.506| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.78 r_work: 0.3325 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8417 Z= 0.094 Angle : 0.498 10.747 11373 Z= 0.257 Chirality : 0.041 0.155 1296 Planarity : 0.004 0.059 1437 Dihedral : 3.879 26.510 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.80 % Allowed : 30.52 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1106 helix: 1.54 (0.29), residues: 355 sheet: -1.17 (0.29), residues: 290 loop : -0.69 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.019 0.001 TYR S 178 PHE 0.021 0.001 PHE R 131 TRP 0.009 0.001 TRP R 175 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8415) covalent geometry : angle 0.49712 (11369) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.18749 ( 4) hydrogen bonds : bond 0.02577 ( 387) hydrogen bonds : angle 4.26828 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.55 seconds wall clock time: 36 minutes 44.70 seconds (2204.70 seconds total)